MobiDB: a comprehensive database of intrinsic protein disorder annotations
Open Access
- 1 June 2012
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 28 (15), 2080-2081
- https://doi.org/10.1093/bioinformatics/bts327
Abstract
Motivation: Disordered protein regions are key to the function of numerous processes within an organism and to the determination of a protein's biological role. The most common source for protein disorder annotations, DisProt, covers only a fraction of the available sequences. Alternatively, the Protein Data Bank (PDB) has been mined for missing residues in X-ray crystallographic structures. Herein, we provide a centralized source for data on different flavours of disorder in protein structures, MobiDB, building on and expanding the content provided by already existing sources. In addition to the DisProt and PDB X-ray structures, we have added experimental information from NMR structures and five different flavours of two disorder predictors (ESpritz and IUpred). These are combined into a weighted consensus disorder used to classify disordered regions into flexible and constrained disorder. Users are encouraged to submit manual annotations through a submission form. MobiDB features experimental annotations for 17 285 proteins, covering the entire PDB and predictions for the SwissProt database, with 565 200 annotated sequences. Depending on the disorder flavour, 6–20% of the residues are predicted as disordered. Availability: The database is freely available at http://mobidb.bio.unipd.it/. Contact:silvio.tosatto@unipd.itKeywords
This publication has 19 references indexed in Scilit:
- ESpritz: accurate and fast prediction of protein disorderBioinformatics, 2011
- Protein disorder—a breakthrough invention of evolution?Current Opinion in Structural Biology, 2011
- Ongoing and future developments at the Universal Protein ResourceNucleic Acids Research, 2010
- MOBI: a web server to define and visualize structural mobility in NMR protein ensemblesBioinformatics, 2010
- The Pfam protein families databaseNucleic Acids Research, 2009
- Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domainProceedings of the National Academy of Sciences, 2008
- DisProt: the Database of Disordered ProteinsNucleic Acids Research, 2006
- The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB dataNucleic Acids Research, 2006
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical featuresBiopolymers, 1983